5TT8

Crystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with benzolamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report



Literature

Structure-Activity Relationship for Sulfonamide Inhibition of Helicobacter pylori alpha-Carbonic Anhydrase.

Modak, J.K.Liu, Y.C.Supuran, C.T.Roujeinikova, A.

(2016) J Med Chem 59: 11098-11109

  • DOI: 10.1021/acs.jmedchem.6b01333
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • α-Carbonic anhydrase of Helicobacter pylori (HpαCA) plays an important role in the acclimation of this oncobacterium to the acidic pH of the stomach. Sulfonamide inhibitors of HpαCA possess anti-H. pylori activity. The crystal structures of complexes ...

    α-Carbonic anhydrase of Helicobacter pylori (HpαCA) plays an important role in the acclimation of this oncobacterium to the acidic pH of the stomach. Sulfonamide inhibitors of HpαCA possess anti-H. pylori activity. The crystal structures of complexes of HpαCA with a family of acetazolamide-related sulfonamides have been determined. Analysis of the structures revealed that the mode of sulfonamide binding correlates well with their inhibitory activities. In addition, comparisons with the corresponding inhibitor complexes of human carbonic anhydrase II (HCAII) indicated that HpαCA possesses an additional, alternative binding site for sulfonamides that is not present in HCAII. Furthermore, the hydrophobic pocket in HCAII that stabilizes the apolar moiety of sulfonamide inhibitors is replaced with a more open, hydrophilic pocket in HpαCA. Thus, our analysis identified major structural features can be exploited in the design of selective and more potent inhibitors of HpαCA that may lead to novel antimicrobials.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University , Clayton, Victoria 3800, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-carbonic anhydrase
A, B, C, D, E, F, G, H
234Helicobacter pylori 26695Mutation(s): 0 
Gene Names: C694_06140
Find proteins for A0A0M3KL20 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  A0A0M3KL20
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D8W
Query on D8W

Download CCD File 
A, B, C, D, E, G, H
5-[(phenylsulfonyl)amino]-1,3,4-thiadiazole-2-sulfonamide
C8 H8 N4 O4 S3
PWDGTQXZLNDOKS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D8WKi:  315   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.24α = 90
b = 134.4β = 90.04
c = 165.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
PHENIXphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release